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Computational Biology, Bioinformatics, and Cheminformatics

CARC supports a wide array of open source and licensed bioinformatics, computational biology, and cheminformatics software on its supercomputing clusters. These include codes for phylogenetic analysis; genomics (sequence alignment, mapping, and processing, SNP/SNV identification, and de novo assembly); molecular dynamics and QM/MM simulation; cheminformatics; and molecular visualization tools. 

Large shared genomic and other databases in regular use by members of a research group can be migrated to and stored on CARC filesystems or on the Research Storage Consortium (RSC) mass storage system. To submit a shared storage request email help@carc.unm.edu.

Custom-designed workshops for specific codes or workflows can be designed in collaboration with CARC Applications Scientists and Systems staff. For inquiries, please contact director@carc.unm.edu

Code/ Software Suite

Purpose

Installed Versions

Machines

Abyss

Sequence assembly

1.3.4, 2.0.2

Wheeler, Xena, TaosPoblano,

Admixture

Ancestry estimation

1.3.0

Wheeler, Xena,

aTRAM

Sequence assembly

2.alpha.3, 2.alpha.5

Wheeler, Taos

AutoDock

Molecular docking

4.2.6

Wheeler, Xena

AutoDock Vina

Molecular docking

1.1.2

Xena

BamTools

Tool for manipulation of BAM files

2.4.1

Wheeler, Taos

BarraCUDA

GPU Accelerated DNA Sequence Alignment. Based on BWA

0.7.0

Xena

BCFtools

Manipulation of BCF and VCF

1.1, 1.4, 1.5

Wheeler, Gibbs, Taos

BEAST

MCMC Bayesian sequence analysis 

2.4.0

Galles

Bedtools2

Tool for genome arthmetic

2.26

Wheeler, Taos

BLAST+

Command line BLAST

2.6.0

Wheeler, Taos

BLAT

BLAST like tool for sequence alignment

2.35

Wheeler, Taos

Bowtie

Sequence alignment

1.1.2, 1.2, 2.1.0, 2.2.3 2.2.6, 2.2.9, 2.3.1

Wheeler, Xena, Gibbs, Poblano

BWA

Mapping low-divergent sequences

0.7.15

Wheeler

Canu

Sequence assembly

1.5, 1.6

Wheeler, Taos

Clustal Omega

Multiple sequence aligner

1.2.4

Wheeler, Taos

ClustalW

Multiple sequence aligner

2.1

Wheeler, Taos

Cufflinks

Sequence assembly

2.2.1

Gibbs, Poblano

DISCOVAR de novo

Sequence assembly

52293

Wheeler, Taos

ExaBayes

Bayesian tree inference

1.5

Wheeler, Taos

FastQC

Quality control on high throughput sequence data

0.11.3, 0.11.5

Wheeler

FFP

Phylogeny comparison

3.19

Wheeler, Taos

FreeBayes

Bayesian genotyping

1.1.0

Wheeler, Taos

GATK

Genome analysis

2.5, 3.2-2

Gibbs, Poblano

GMAP

Genomic Mapping and Alignment

 

Wheeler

GSNAP

Sequence alignment

2013-04-14, 2013-09-11,, 2017-06-16

Wheeler, Poblano,Galles

MrBayes

Bayesian inference of phylogeny

3.2.6

Galles

PAML

Phylogenetic analysis 

4.8, 4.9

Wheeler, Taos, Galles,

PRISM

Split read mapping

1.1.6

Gibbs

RAxML

Parallel phylogenetic inference

8.1.17, 8.2.11

Wheeler, Galles, Taos

SAMTools

Sequence alignment and mapping

0.1.9, 1.1, 1.2, 1.3.1, 1.4, 1.5, 1.6

Wheeler, Xena, Gibbs, Galles, Taos

SOAPdenovo

Sequence assembly

2.4

Wheeler, Xena, Taos

SPAdes

Sequence assembly

3.10.1, 3.1131

Wheeler, Xena, Taos

STAR

RNAseq aligner

2.3.0, 2.4.0, 2.4.2, 2.5.3

Wheeler, Xena, Gibbs, Taos

Strelka

Variant caller

2.8.2

Wheeler, Taos

TopHat

Splice junction mapper

2.0.9

Poblano

Velvet

Short read sequence assembly

1.2.08, 1.2.10

Wheeler, Xena, Galles, Gibbs, Poblano, Taos

Trinity

RNAseq assembler

2.1.1

Xena

To request additional software installation please email help@carc.unm.edu.